2,209 results on '"Lazar, Alexander J"'
Search Results
2. Patterns of Care and Outcomes of Patients with Small Gastrointestinal Stromal Tumors at a High-Volume Sarcoma Center
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Lyu, Heather G., Witt, Russell G., Rajkot, Nikita, Keung, Emily Z., Torres, Keila E., Hunt, Kelly K., Somaiah, Neeta, Lazar, Alexander J., Roland, Christina L., and Scally, Christopher P.
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- 2024
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3. ASO Visual Abstract: Clinical Variables Influencing Outcomes in Patients with Atypical Intradermal Smooth Muscle Neoplasms (Formerly Cutaneous Leiomyosarcomas)—Single-Institution Study of 95 Surgical Patients
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Gingrich, Alicia, Wangsiricharoen, Sintawat, Torres, Madeline B., Ravi, Vinod, Ratan, Ravin, Keung, Emily Z., Scally, Christopher P., Lazar, Alexander J., Wang, Wei-Lien, Roland, Christina L., Hunt, Kelly K., Yu, Wendong, and Torres, Keila E.
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- 2024
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4. ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97
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Pozner, Amir, Li, Li, Verma, Shiv Prakash, Wang, Shuxin, Barrott, Jared J., Nelson, Mary L., Yu, Jamie S. E., Negri, Gian Luca, Colborne, Shane, Hughes, Christopher S., Zhu, Ju-Fen, Lambert, Sydney L., Carroll, Lara S., Smith-Fry, Kyllie, Stewart, Michael G., Kannan, Sarmishta, Jensen, Bodrie, John, Cini M., Sikdar, Saif, Liu, Hongrui, Dang, Ngoc Ha, Bourdage, Jennifer, Li, Jinxiu, Vahrenkamp, Jeffery M., Mortenson, Katelyn L., Groundland, John S., Wustrack, Rosanna, Senger, Donna L., Zemp, Franz J., Mahoney, Douglas J., Gertz, Jason, Zhang, Xiaoyang, Lazar, Alexander J., Hirst, Martin, Morin, Gregg B., Nielsen, Torsten O., Shen, Peter S., and Jones, Kevin B.
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- 2024
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5. A randomized, non-comparative phase 2 study of neoadjuvant immune-checkpoint blockade in retroperitoneal dedifferentiated liposarcoma and extremity/truncal undifferentiated pleomorphic sarcoma
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Roland, Christina L., Nassif Haddad, Elise F., Keung, Emily Z., Wang, Wei-Lien, Lazar, Alexander J., Lin, Heather, Chelvanambi, Manoj, Parra, Edwin R., Wani, Khalida, Guadagnolo, B. Ashleigh, Bishop, Andrew J., Burton, Elizabeth M., Hunt, Kelly K., Torres, Keila E., Feig, Barry W., Scally, Christopher P., Lewis, Valerae O., Bird, Justin E., Ratan, Ravin, Araujo, Dejka, Zarzour, M. Alexandra, Patel, Shreyaskumar, Benjamin, Robert, Conley, Anthony P., Livingston, J. Andrew, Ravi, Vinod, Tawbi, Hussein A., Lin, Patrick P., Moon, Bryan S., Satcher, Robert L., Mujtaba, Bilal, Witt, Russell G., Traweek, Raymond S., Cope, Brandon, Lazcano, Rossana, Wu, Chia-Chin, Zhou, Xiao, Mohammad, Mohammad M., Chu, Randy A., Zhang, Jianhua, Damania, Ashish, Sahasrabhojane, Pranoti, Tate, Taylor, Callahan, Kate, Nguyen, Sa, Ingram, Davis, Morey, Rohini, Crosby, Shadarra, Mathew, Grace, Duncan, Sheila, Lima, Cibelle F., Blay, Jean-Yves, Fridman, Wolf Herman, Shaw, Kenna, Wistuba, Ignacio, Futreal, Andrew, Ajami, Nadim, Wargo, Jennifer A., and Somaiah, Neeta
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- 2024
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6. International Multicenter Retrospective Study From the Ultra-rare Sarcoma Working Group on Low-grade Fibromyxoid Sarcoma, Sclerosing Epithelioid Fibrosarcoma, and Hybrid Forms: Outcome of Primary Localized Disease
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Giani, Claudia, Salawu, Abdulazeez, Ljevar, Silva, Denu, Ryan A., Napolitano, Andrea, Palmerini, Emanuela, Connolly, Elizabeth A., Ogura, Koichi, Wong, Daniel D., Scanferla, Roberto, Rosenbaum, Evan, Bajpai, Jyoti, Li, Zola Chia-Chen, Bae, Susie, D’Ambrosio, Lorenzo, Bialick, Steve, Wagner, Andrew J., Lee, Alexander T.J., Koseła-Paterczyk, Hanna, Baldi, Giacomo G., Brunello, Antonella, Lee, Yeh Chen, Loong, Herbert H., Boikos, Sosipatros, Campos, Fernando, Cicala, Carlo M., Maki, Robert G., Hindi, Nadia, Figura, Costanza, Almohsen, Shahd S., Patel, Sheyaskumar, Jones, Robin L., Ibrahim, Toni, Karim, Rooshdiya, Kawai, Akira, Carey-Smith, Richard, Boyle, Richard, Taverna, Silvia M., Lazar, Alexander J., Demicco, Elizabeth G., Bovee, Judith V.M.G., Dei Tos, Angelo P., Fletcher, Christopher, Baumhoer, Daniel, Sbaraglia, Marta, Schaefer, Inga-Marie, Miceli, Rosalba, Gronchi, Alessandro, and Stacchiotti, Silvia
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- 2024
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7. ASO Visual Abstract: Patterns of Care and Outcomes for Patients With Small Gastrointestinal Stromal Tumors at a High-Volume Sarcoma Center
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Lyu, Heather G., Witt, Russell G., Rajkot, Nikita, Keung, Emily Z., Torres, Keila E., Hunt, Kelly K., Somaiah, Neeta, Lazar, Alexander J., Roland, Christina L., and Scally, Christopher P.
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- 2024
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8. Revision of the Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis Classification Schema for Melanocytic Lesions
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Barnhill, Raymond L, Elder, David E, Piepkorn, Michael W, Knezevich, Stevan R, Reisch, Lisa M, Eguchi, Megan M, Bastian, Boris C, Blokx, Willeke, Bosenberg, Marcus, Busam, Klaus J, Carr, Richard, Cochran, Alistair, Cook, Martin G, Duncan, Lyn M, Elenitsas, Rosalie, de la Fouchardière, Arnaud, Gerami, Pedram, Johansson, Iva, Ko, Jennifer, Landman, Gilles, Lazar, Alexander J, Lowe, Lori, Massi, Daniela, Messina, Jane, Mihic-Probst, Daniela, Parker, Douglas C, Schmidt, Birgitta, Shea, Christopher R, Scolyer, Richard A, Tetzlaff, Michael, Xu, Xiaowei, Yeh, Iwei, Zembowicz, Artur, and Elmore, Joann G
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Health Services and Systems ,Biomedical and Clinical Sciences ,Health Sciences ,Clinical Research ,Cancer ,Humans ,Skin Neoplasms ,Melanoma ,Pathologists ,Consensus ,Health Facilities ,Biomedical and clinical sciences ,Health sciences - Abstract
ImportanceA standardized pathology classification system for melanocytic lesions is needed to aid both pathologists and clinicians in cataloging currently existing diverse terminologies and in the diagnosis and treatment of patients. The Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis (MPATH-Dx) has been developed for this purpose.ObjectiveTo revise the MPATH-Dx version 1.0 classification tool, using feedback from dermatopathologists participating in the National Institutes of Health-funded Reducing Errors in Melanocytic Interpretations (REMI) Study and from members of the International Melanoma Pathology Study Group (IMPSG).Evidence reviewPracticing dermatopathologists recruited from 40 US states participated in the 2-year REMI study and provided feedback on the MPATH-Dx version 1.0 tool. Independently, member dermatopathologists participating in an IMPSG workshop dedicated to the MPATH-Dx schema provided additional input for refining the MPATH-Dx tool. A reference panel of 3 dermatopathologists, the original authors of the MPATH-Dx version 1.0 tool, integrated all feedback into an updated and refined MPATH-Dx version 2.0.FindingsThe new MPATH-Dx version 2.0 schema simplifies the original 5-class hierarchy into 4 classes to improve diagnostic concordance and to provide more explicit guidance in the treatment of patients. This new version also has clearly defined histopathological criteria for classification of classes I and II lesions; has specific provisions for the most frequently encountered low-cumulative sun damage pathway of melanoma progression, as well as other, less common World Health Organization pathways to melanoma; provides guidance for classifying intermediate class II tumors vs melanoma; and recognizes a subset of pT1a melanomas with very low risk and possible eventual reclassification as neoplasms lacking criteria for melanoma.Conclusions and relevanceThe implementation of the newly revised MPATH-Dx version 2.0 schema into clinical practice is anticipated to provide a robust tool and adjunct for standardized diagnostic reporting of melanocytic lesions and management of patients to the benefit of both health care practitioners and patients.
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- 2023
9. Analysis of germline-driven ancestry-associated gene expression in cancers
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Chambwe, Nyasha, Sayaman, Rosalyn W, Hu, Donglei, Huntsman, Scott, Network, The Cancer Genome Analysis, Carrot-Zhang, Jian, Berger, Ashton C, Han, Seunghun, Meyerson, Matthew, Damrauer, Jeffrey S, Hoadley, Katherine A, Felau, Ina, Demchok, John A, Mensah, Michael KA, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Knijnenburg, Theo A, Robertson, A Gordon, Yau, Christina, Benz, Christopher, Huang, Kuan-lin, Newberg, Justin Y, Frampton, Garrett M, Mashl, R Jay, Ding, Li, Romanel, Alessandro, Demichelis, Francesca, Zhou, Wanding, Laird, Peter W, Shen, Hui, Wong, Christopher K, Stuart, Joshua M, Lazar, Alexander J, Le, Xiuning, Oak, Ninad, Kemal, Anab, Caesar-Johnson, Samantha, Zenklusen, Jean C, Ziv, Elad, Beroukhim, Rameen, and Cherniack, Andrew D
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Biological Sciences ,Health Sciences ,Genetics ,Human Genome ,Biotechnology ,Cancer ,Good Health and Well Being ,Gene Expression ,Germ Cells ,Humans ,Neoplasms ,Quantitative Trait Loci ,RNA ,Messenger ,Cancer Genome Analysis Network ,Bioinformatics ,Computer sciences ,Genomics ,RNAseq ,Sequence analysis - Abstract
Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecular differences across ancestry groups. Using multi-omics datasets from The Cancer Genome Atlas (TCGA), we enumerate ancestry-informative markers colocalized with cancer-type-specific expression quantitative trait loci (e-QTLs) at ancestry-associated genes. This approach is generalizable to other settings with paired germline genotyping and mRNA expression data for a multi-ethnic cohort. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020), Robertson et al. (2021), and Sayaman et al. (2021).
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- 2022
10. Epigenomic and Transcriptomic Profiling of Solitary Fibrous Tumors Identifies Site-Specific Patterns and Candidate Genes Regulated by DNA Methylation
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Beird, Hannah C., Cloutier, Jeffrey M., Gokgoz, Nalan, Eeles, Christopher, Griffin, Anthony M., Ingram, Davis R., Wani, Khalida M., Segura, Rossana Lazcano, Cohen, Luca, Ho, Carl, Wunder, Jay S., Andrulis, Irene L., Futreal, P. Andrew, Haibe-Kains, Benjamin, Lazar, Alexander J., Wang, Wei-Lien, Przybyl, Joanna, and Demicco, Elizabeth G.
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- 2024
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11. TRPS1 expression in MPNST is correlated with PRC2 inactivation and loss of H3K27me3
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Lazcano, Rossana, Ingram, Davis R., Panse, Gauri, Lazar, Alexander J., Wang, Wei-Lien, and Cloutier, Jeffrey M.
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- 2024
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12. Correction: “The 5th edition of The World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms” Leukemia. 2022 Jul;36(7):1720–1748
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Alaggio, Rita, Amador, Catalina, Anagnostopoulos, Ioannis, Attygalle, Ayoma D., de Oliveira Araujo, Iguaracyra Barreto, Berti, Emilio, Bhagat, Govind, Borges, Anita Maria, Boyer, Daniel, Calaminici, Mariarita, Chadburn, Amy, Chan, John K. C., Cheuk, Wah, Chng, Wee-Joo, Choi, John K., Chuang, Shih-Sung, Coupland, Sarah E., Czader, Magdalena, Dave, Sandeep S., de Jong, Daphne, Di Napoli, Arianna, Du, Ming-Qing, Elenitoba-Johnson, Kojo S., Ferry, Judith, Geyer, Julia, Gratzinger, Dita, Guitart, Joan, Gujral, Sumeet, Harris, Marian, Harrison, Christine J., Hartmann, Sylvia, Hochhaus, Andreas, Jansen, Patty M., Karube, Kennosuke, Kempf, Werner, Khoury, Joseph, Kimura, Hiroshi, Klapper, Wolfram, Kovach, Alexandra E., Kumar, Shaji, Lazar, Alexander J., Lazzi, Stefano, Leoncini, Lorenzo, Leung, Nelson, Leventaki, Vasiliki, Li, Xiao-Qiu, Lim, Megan S., Liu, Wei-Ping, Louissaint, Jr, Abner, Marcogliese, Andrea, Medeiros, L. Jeffrey, Michal, Michael, Miranda, Roberto N., Mitteldorf, Christina, Montes-Moreno, Santiago, Morice, William, Nardi, Valentina, Naresh, Kikkeri N., Natkunam, Yasodha, Ng, Siok-Bian, Oschlies, Ilske, Ott, German, Parrens, Marie, Pulitzer, Melissa, Rajkumar, S. Vincent, Rawstron, Andrew C., Rech, Karen, Rosenwald, Andreas, Said, Jonathan, Sarkozy, Clémentine, Sayed, Shahin, Saygin, Caner, Schuh, Anna, Sewell, William, Siebert, Reiner, Sohani, Aliyah R., Suzuki, Ritsuro, Tooze, Reuben, Traverse-Glehen, Alexandra, Vega, Francisco, Vergier, Beatrice, Wechalekar, Ashutosh D., Wood, Brent, Xerri, Luc, and Xiao, Wenbin
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- 2023
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13. The Impact of Next-generation Sequencing on Interobserver Agreement and Diagnostic Accuracy of Desmoplastic Melanocytic Neoplasms
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Chen, Alice, Sharma, Natasha, Patel, Pragi, Olivares, Shantel, Bahrami, Armita, Barnhill, Raymond L., Blokx, Willeke A.M., Bosenberg, Marcus, Busam, Klaus J., de La Fouchardière, Arnaud, Duncan, Lyn M., Elder, David E., Ko, Jennifer S., Landman, Gilles, Lazar, Alexander J., Lezcano, Cecilia, Lowe, Lori, Maher, Nigel, Massi, Daniela, Messina, Jane, Mihic-Probst, Daniela, Parker, Douglas C., Redpath, Margaret, Scolyer, Richard A., Shea, Christopher R., Spatz, Alan, Tron, Victor, Xu, Xiaowei, Yeh, Iwei, Jung Yun, Sook, Zembowicz, Artur, and Gerami, Pedram
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- 2024
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14. DNA mismatch repair deficiency as a biomarker in sarcoma
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Denu, Ryan A., Quintana-Perez, Christopher D., Wangsiricharoen, Sintawat, Ingram, Davis R., Wani, Khalida M., Lazar, Alexander J., Ratan, Ravin, Roland, Christina L., and You, Y. Nancy
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- 2024
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15. The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Lymphoid Neoplasms
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Alaggio, Rita, Amador, Catalina, Anagnostopoulos, Ioannis, Attygalle, Ayoma D, Araujo, Iguaracyra Barreto de Oliveira, Berti, Emilio, Bhagat, Govind, Borges, Anita Maria, Boyer, Daniel, Calaminici, Mariarita, Chadburn, Amy, Chan, John KC, Cheuk, Wah, Chng, Wee-Joo, Choi, John K, Chuang, Shih-Sung, Coupland, Sarah E, Czader, Magdalena, Dave, Sandeep S, de Jong, Daphne, Du, Ming-Qing, Elenitoba-Johnson, Kojo S, Ferry, Judith, Geyer, Julia, Gratzinger, Dita, Guitart, Joan, Gujral, Sumeet, Harris, Marian, Harrison, Christine J, Hartmann, Sylvia, Hochhaus, Andreas, Jansen, Patty M, Karube, Kennosuke, Kempf, Werner, Khoury, Joseph, Kimura, Hiroshi, Klapper, Wolfram, Kovach, Alexandra E, Kumar, Shaji, Lazar, Alexander J, Lazzi, Stefano, Leoncini, Lorenzo, Leung, Nelson, Leventaki, Vasiliki, Li, Xiao-Qiu, Lim, Megan S, Liu, Wei-Ping, Louissaint, Abner, Marcogliese, Andrea, Medeiros, L Jeffrey, Michal, Michael, Miranda, Roberto N, Mitteldorf, Christina, Montes-Moreno, Santiago, Morice, William, Nardi, Valentina, Naresh, Kikkeri N, Natkunam, Yasodha, Ng, Siok-Bian, Oschlies, Ilske, Ott, German, Parrens, Marie, Pulitzer, Melissa, Rajkumar, S Vincent, Rawstron, Andrew C, Rech, Karen, Rosenwald, Andreas, Said, Jonathan, Sarkozy, Clémentine, Sayed, Shahin, Saygin, Caner, Schuh, Anna, Sewell, William, Siebert, Reiner, Sohani, Aliyah R, Tooze, Reuben, Traverse-Glehen, Alexandra, Vega, Francisco, Vergier, Beatrice, Wechalekar, Ashutosh D, Wood, Brent, Xerri, Luc, and Xiao, Wenbin
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Cancer ,Hematologic Neoplasms ,Humans ,Lymphoma ,World Health Organization ,Clinical Sciences ,Oncology and Carcinogenesis ,Immunology - Abstract
We herein present an overview of the upcoming 5th edition of the World Health Organization Classification of Haematolymphoid Tumours focussing on lymphoid neoplasms. Myeloid and histiocytic neoplasms will be presented in a separate accompanying article. Besides listing the entities of the classification, we highlight and explain changes from the revised 4th edition. These include reorganization of entities by a hierarchical system as is adopted throughout the 5th edition of the WHO classification of tumours of all organ systems, modification of nomenclature for some entities, revision of diagnostic criteria or subtypes, deletion of certain entities, and introduction of new entities, as well as inclusion of tumour-like lesions, mesenchymal lesions specific to lymph node and spleen, and germline predisposition syndromes associated with the lymphoid neoplasms.
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- 2022
16. BRAF Mutated and Morphologically Spitzoid Tumors, a Subgroup of Melanocytic Neoplasms Difficult to Distinguish From True Spitz Neoplasms
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Gerami, Pedram, Chen, Alice, Sharma, Natasha, Patel, Pragi, Hagstrom, Michael, Kancherla, Pranav, Geraminejad, Tara, Olivares, Shantel, Biswas, Asok, Bosenberg, Marcus, Busam, Klaus J., de La Fouchardière, Arnaud, Duncan, Lyn M., Elder, David E., Ko, Jennifer, Landman, Gilles, Lazar, Alexander J., Lowe, Lori, Massi, Daniela, Mihic-Probst, Daniela, Parker, Douglas C., Scolyer, Richard A., Shea, Christopher R., Zembowicz, Artur, Yun, Sook Jung, Blokx, Willeke A.M., and Barnhill, Raymond L.
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- 2024
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17. Appropriate use criteria for ancillary diagnostic testing in dermatopathology: New recommendations for 11 tests and 220 clinical scenarios from the American Society of Dermatopathology Appropriate Use Criteria Committee
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Members, AUC Committee, Fung, Maxwell A, Vidal, Claudia I, Armbrecht, Eric A, Andea, Aleodor A, Cassarino, David S, Comfere, Nneka I, Emanuel, Patrick O, Ferringer, Tammie, Hristov, Alexandra C, Kim, Jinah, Lauer, Scott R, Linos, Konstantinos, Missall, Tricia A, Motaparthi, Kiran, Novoa, Roberto A, Patel, Rajiv, Shalin, Sara C, Sundram, Uma, Panel, Rating, Calame, Antoanella, Bennett, Daniel D, Duncan, Lyn M, Elston, Dirk M, Hosler, Gregory A, Hurley, Yadira M, Lazar, Alexander J, Lowe, Lori, Messina, Jane, Myles, Jonathan, Plaza, Jose A, Prieto, Victor G, Reddy, Vijaya, Schaffer, András, and Subtil, Antonio
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Clinical Research ,Dermatology ,Evidence-Based Medicine ,Humans ,Pathology ,Clinical ,Skin Diseases ,Societies ,Medical ,United States ,ancillary studies ,angiosarcoma ,appropriate use criteria ,choosing wisely ,cMYC ,dermatitis ,dermatology ,dermatopathology ,dermatophytosis ,diagnosis ,evidence-based medicine ,expert rating ,Gomori methenamine silver ,Grocott-Gomori ,immunohistochemistry ,in situ hybridization ,kappa ,lambda ,lymphoma ,onychomycosis ,pathology ,periodic acid-Schiff ,RAND ,UCLA appropriateness method ,TERT promoter ,tinea ,AUC Committee Members ,Rating Panel ,Grocott-Gömöri ,Gömöri methenamine silver ,RAND/UCLA appropriateness method ,Clinical Sciences ,Dermatology & Venereal Diseases ,Clinical sciences - Abstract
BackgroundAppropriate use criteria (AUC) provide patient-centered physician guidance in test selection. An initial set of AUC was reported by the American Society of Dermatopathology (ASDP) in 2018. AUC reflect evidence collected at single timepoints and may be affected by evolving evidence and experience. The objective of this study was to update and expand AUC for selected tests.MethodsRAND/UCLA (RAND Corporation [Santa Monica, CA]/University of California Los Angeles) methodology used includes the following: (a) literature review; (b) review of previously rated tests and previously employed clinical scenarios; (c) selection of previously rated tests for new ratings; (d) development of new clinical scenarios; (e) selection of additional tests; (f) three rating rounds with feedback and group discussion after rounds 1 and 2.ResultsFor 220 clinical scenarios comprising lymphoproliferative (light chain clonality), melanocytic (comparative genomic hybridization, fluorescence in situ hybridization, reverse transcription polymerase chain reaction, telomerase reverse transcriptase promoter), vascular disorders (MYC), and inflammatory dermatoses (periodic acid-Schiff, Gömöri methenamine silver), consensus by panel raters was reached in 172 of 220 (78%) scenarios, with 103 of 148 (70%) rated "usually appropriate" or "rarely appropriate" and 45 of 148 (30%), "appropriateness uncertain."LimitationsThe study design only measures appropriateness. Cost, availability, test comparison, and additional clinical considerations are not measured. The possibility that the findings of this study may be influenced by the inherent biases of the dermatopathologists involved in the study cannot be excluded.ConclusionsAUC are reported for selected diagnostic tests in clinical scenarios that occur in dermatopathology practice. Adhering to AUC may reduce inappropriate test utilization and improve healthcare delivery.
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- 2022
18. Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells
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Goyal, Yogesh, Busch, Gianna T., Pillai, Maalavika, Li, Jingxin, Boe, Ryan H., Grody, Emanuelle I., Chelvanambi, Manoj, Dardani, Ian P., Emert, Benjamin, Bodkin, Nicholas, Braun, Jonas, Fingerman, Dylan, Kaur, Amanpreet, Jain, Naveen, Ravindran, Pavithran T., Mellis, Ian A., Kiani, Karun, Alicea, Gretchen M., Fane, Mitchell E., Ahmed, Syeda Subia, Li, Haiyin, Chen, Yeqing, Chai, Cedric, Kaster, Jessica, Witt, Russell G., Lazcano, Rossana, Ingram, Davis R., Johnson, Sarah B., Wani, Khalida, Dunagin, Margaret C., Lazar, Alexander J., Weeraratna, Ashani T., Wargo, Jennifer A., Herlyn, Meenhard, and Raj, Arjun
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- 2023
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19. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance
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Chu, Yanshuo, Dai, Enyu, Li, Yating, Han, Guangchun, Pei, Guangsheng, Ingram, Davis R., Thakkar, Krupa, Qin, Jiang-Jiang, Dang, Minghao, Le, Xiuning, Hu, Can, Deng, Qing, Sinjab, Ansam, Gupta, Pravesh, Wang, Ruiping, Hao, Dapeng, Peng, Fuduan, Yan, Xinmiao, Liu, Yunhe, Song, Shumei, Zhang, Shaojun, Heymach, John V., Reuben, Alexandre, Elamin, Yasir Y., Pizzi, Melissa P., Lu, Yang, Lazcano, Rossana, Hu, Jian, Li, Mingyao, Curran, Michael, Futreal, Andrew, Maitra, Anirban, Jazaeri, Amir A., Ajani, Jaffer A., Swanton, Charles, Cheng, Xiang-Dong, Abbas, Hussein A., Gillison, Maura, Bhat, Krishna, Lazar, Alexander J., Green, Michael, Litchfield, Kevin, Kadara, Humam, Yee, Cassian, and Wang, Linghua
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- 2023
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20. Comprehensive proteogenomic characterization of rare kidney tumors
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Lazar, Alexander J., Paulovich, Amanda G., Antczak, Andrzej, Green, Anthony, Ma’ayan, Avi, Pruetz, Barb, Zhang, Bing, Reva, Boris, Druker, Brian J., Goldthwaite, Charles A., Jr., Birger, Chet, Mani, D.R., Chesla, David, Fenyö, David, Schadt, Eric E., Wilson, George, Kołodziejczak, Iga, John, Ivy, Hafron, Jason, Vo, Josh, Zaalishvili, Kakhaber, Ketchum, Karen A., Rodland, Karin D., Nyce, Kristen, Wiznerowicz, Maciej, Domagalski, Marcin J., Anurag, Meenakshi, Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Edwards, Nathan J., Vatanian, Negin, VanderKolk, Pamela, McGarvey, Peter B., Dhir, Rajiv, Thangudu, Ratna R., Crispen, Reese, Smith, Richard D., Payne, Samuel H., Cottingham, Sandra, Cai, Shuang, Carr, Steven A., Liu, Tao, Le, Toan, Ma, Weiping, Zhang, Xu, Lu, Yin, Shutack, Yvonne, Zhang, Zhen, Li, Ginny Xiaohe, Chen, Lijun, Hsiao, Yi, Mannan, Rahul, Zhang, Yuping, Luo, Jie, Petralia, Francesca, Cho, Hanbyul, Hosseini, Noshad, Leprevost, Felipe da Veiga, Calinawan, Anna, Li, Yize, Anand, Shankara, Dagar, Aniket, Geffen, Yifat, Kumar-Sinha, Chandan, Chugh, Seema, Le, Anne, Ponce, Sean, Guo, Shenghao, Zhang, Cissy, Schnaubelt, Michael, Al Deen, Nataly Naser, Chen, Feng, Caravan, Wagma, Houston, Andrew, Hopkins, Alex, Newton, Chelsea J., Wang, Xiaoming, Polasky, Daniel A., Haynes, Sarah, Yu, Fengchao, Jing, Xiaojun, Chen, Siqi, Robles, Ana I., Mesri, Mehdi, Thiagarajan, Mathangi, An, Eunkyung, Getz, Gad A., Linehan, W. Marston, Hostetter, Galen, Jewell, Scott D., Chan, Daniel W., Wang, Pei, Omenn, Gilbert S., Mehra, Rohit, Ricketts, Christopher J., Ding, Li, Chinnaiyan, Arul M., Cieslik, Marcin P., Dhanasekaran, Saravana M., Zhang, Hui, and Nesvizhskii, Alexey I.
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- 2024
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21. Updates on WHO classification for small round cell tumors: Ewing sarcoma vs. everything else
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Dehner, Carina A., Lazar, Alexander J., and Chrisinger, John S.A.
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- 2024
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22. Glycoprotein Nonmetastatic Melanoma Protein B (GPNMB) Immunohistochemistry Can Be a Useful Ancillary Tool to Identify Perivascular Epithelioid Cell Tumor
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Wangsiricharoen, Sintawat, Ingram, Davis R., Morey, Rohini R., Wani, Khalida, Lazar, Alexander J., and Wang, Wei-Lien
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- 2024
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23. Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma
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Gounder, Mrinal M, Agaram, Narasimhan P, Trabucco, Sally E, Robinson, Victoria, Ferraro, Richard A, Millis, Sherri Z, Krishnan, Anita, Lee, Jessica, Attia, Steven, Abida, Wassim, Drilon, Alexander, Chi, Ping, Angelo, Sandra P D’, Dickson, Mark A, Keohan, Mary Lou, Kelly, Ciara M, Agulnik, Mark, Chawla, Sant P, Choy, Edwin, Chugh, Rashmi, Meyer, Christian F, Myer, Parvathi A, Moore, Jessica L, Okimoto, Ross A, Pollock, Raphael E, Ravi, Vinod, Singh, Arun S, Somaiah, Neeta, Wagner, Andrew J, Healey, John H, Frampton, Garrett M, Venstrom, Jeffrey M, Ross, Jeffrey S, Ladanyi, Marc, Singer, Samuel, Brennan, Murray F, Schwartz, Gary K, Lazar, Alexander J, Thomas, David M, Maki, Robert G, Tap, William D, Ali, Siraj M, and Jin, Dexter X
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Clinical Sciences ,Oncology and Carcinogenesis ,Cancer ,Biotechnology ,Clinical Research ,Human Genome ,Genetic Testing ,Aetiology ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Biomarkers ,Tumor ,Bone Neoplasms ,Genomics ,Humans ,Mutation ,Osteosarcoma ,Prospective Studies ,Sarcoma - Abstract
There are more than 70 distinct sarcomas, and this diversity complicates the development of precision-based therapeutics for these cancers. Prospective comprehensive genomic profiling could overcome this challenge by providing insight into sarcomas' molecular drivers. Through targeted panel sequencing of 7494 sarcomas representing 44 histologies, we identify highly recurrent and type-specific alterations that aid in diagnosis and treatment decisions. Sequencing could lead to refinement or reassignment of 10.5% of diagnoses. Nearly one-third of patients (31.7%) harbor potentially actionable alterations, including a significant proportion (2.6%) with kinase gene rearrangements; 3.9% have a tumor mutational burden ≥10 mut/Mb. We describe low frequencies of microsatellite instability (
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- 2022
24. Analytical protocol to identify local ancestry-associated molecular features in cancer
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Carrot-Zhang, Jian, Han, Seunghun, Zhou, Wanding, Damrauer, Jeffrey S, Kemal, Anab, Network, Cancer Genome Atlas Analysis, Berger, Ashton C, Meyerson, Matthew, Hoadley, Katherine A, Felau, Ina, Caesar-Johnson, Samantha, Demchok, John A, Mensah, Michael KA, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C, Chambwe, Nyasha, Knijnenburg, Theo A, Robertson, A Gordon, Yau, Christina, Benz, Christopher, Huang, Kuan-lin, Newberg, Justin, Frampton, Garret, Mashl, R Jay, Ding, Li, Romanel, Alessandro, Demichelis, Francesca, Sayaman, Rosalyn W, Ziv, Elad, Laird, Peter W, Shen, Hui, Wong, Christopher K, Stuart, Joshua M, Lazar, Alexander J, Le, Xiuning, Oak, Ninad, Cherniack, Andrew D, and Beroukhim, Rameen
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Health Sciences ,Oncology and Carcinogenesis ,Health Disparities ,Human Genome ,Cancer ,Cancer Genomics ,Minority Health ,4.1 Discovery and preclinical testing of markers and technologies ,2.1 Biological and endogenous factors ,Genetics ,Population ,Genome ,Human ,Genomics ,Genotyping Techniques ,Humans ,Neoplasms ,Phenotype ,Cancer Genome Atlas Analysis Network ,Bioinformatics - Abstract
People of different ancestries vary in cancer risk and outcome, and their molecular differences may indicate sources of these variations. Determining the "local" ancestry composition at each genetic locus across ancestry-admixed populations can suggest causal associations. We present a protocol to identify local ancestry and detect the associated molecular changes, using data from the Cancer Genome Atlas. This workflow can be applied to cancer cohorts with matched tumor and normal data from admixed patients to examine germline contributions to cancer. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020).
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- 2021
25. Pan-cancer proteogenomics characterization of tumor immunity
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Abelin, Jennifer, Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cao, Song, Carr, Steven A., Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Ding, Li, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Heiman, David I., Hong, Runyu, Hu, Yingwei, Huang, Chen, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, McDermott, Jason, McKerrow, Wilson, Mesri, Mehdi, Mumphrey, Michael Brodie, Newton, Chelsea J., Oldroyd, Robert, Payne, Samuel H., Pugliese, Pietro, Rodland, Karin D., Rodrigues, Fernanda Martins, Ruggles, Kelly V., Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Feng, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Li, Qing Kay, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Petralia, Francesca, Ma, Weiping, Yaron, Tomer M., Caruso, Francesca Pia, Tignor, Nicole, Wang, Joshua M., Charytonowicz, Daniel, Johnson, Jared L., Huntsman, Emily M., Marino, Giacomo B., Calinawan, Anna, Evangelista, John Erol, Selvan, Myvizhi Esai, Chowdhury, Shrabanti, Rykunov, Dmitry, Krek, Azra, Song, Xiaoyu, Turhan, Berk, Christianson, Karen E., Lewis, David A., Deng, Eden Z., Clarke, Daniel J.B., Whiteaker, Jeffrey R., Kennedy, Jacob J., Zhao, Lei, Segura, Rossana Lazcano, Batra, Harsh, Raso, Maria Gabriela, Parra, Edwin Roger, Soundararajan, Rama, Tang, Ximing, Li, Yize, Yi, Xinpei, Satpathy, Shankha, Wang, Ying, Wiznerowicz, Maciej, González-Robles, Tania J., Iavarone, Antonio, Gosline, Sara J.C., Reva, Boris, Robles, Ana I., Nesvizhskii, Alexey I., Mani, D.R., Gillette, Michael A., Klein, Robert J., Cieslik, Marcin, Zhang, Bing, Paulovich, Amanda G., Sebra, Robert, Gümüş, Zeynep H., Hostetter, Galen, Fenyö, David, Omenn, Gilbert S., Cantley, Lewis C., Ma'ayan, Avi, Lazar, Alexander J., Ceccarelli, Michele, and Wang, Pei
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- 2024
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26. GLI1-Altered Mesenchymal Tumors With ACTB or PTCH1 Fusion: A Molecular and Clinicopathologic Analysis
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Kerr, Darcy A., Cloutier, Jeffrey M., Margolis, Matthew, Mata, Douglas A., Rodrigues Simoes, Nathalie J., Faquin, William C., Dias-Santagata, Dora, Chopra, Shefali, Charville, Gregory W., Wangsiricharoen, Sintawat, Lazar, Alexander J., Wang, Wei-Lien, Rosenberg, Andrew E., and Tse, Julie Y.
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- 2024
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27. Complete loss of TP53 and RB1 is associated with complex genome and low immune infiltrate in pleomorphic rhabdomyosarcoma
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Beird, Hannah C., Wu, Chia-Chin, Nakazawa, Michael, Ingram, Davis, Daniele, Joseph R., Lazcano, Rossana, Little, Latasha, Davies, Christopher, Daw, Najat C., Wani, Khalida, Wang, Wei-Lien, Song, Xingzhi, Gumbs, Curtis, Zhang, Jianhua, Rubin, Brian, Conley, Anthony, Flanagan, Adrienne M., Lazar, Alexander J., and Futreal, P. Andrew
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- 2023
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28. Deep learning integrates histopathology and proteogenomics at a pan-cancer level
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Aguet, François, Akiyama, Yo, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cantley, Lewis C., Cao, Song, Carr, Steven A., Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Clauser, Karl R., Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Heiman, David I., Hiltke, Tara, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Iavarone, Antonio, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Johnson, Jared L., Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, Rodrigues, Fernanda Martins, McKerrow, Wilson, Mesri, Mehdi, Nesvizhskii, Alexey I., Newton, Chelsea J., Oldroyd, Robert, Paulovich, Amanda G., Payne, Samuel H., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rykunov, Dmitry, Satpathy, Shankha, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Tignor, Nicole, Wang, Liang-Bo, Wang, Pei, Wang, Ying, Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yaron, Tomer M., Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Wang, Joshua M., Hong, Runyu, Demicco, Elizabeth G., Tan, Jimin, Lazcano, Rossana, Moreira, Andre L., Li, Yize, Calinawan, Anna, Razavian, Narges, Schraink, Tobias, Gillette, Michael A., Omenn, Gilbert S., An, Eunkyung, Rodriguez, Henry, Tsirigos, Aristotelis, Ruggles, Kelly V., Ding, Li, Robles, Ana I., Mani, D.R., Rodland, Karin D., Lazar, Alexander J., Liu, Wenke, and Fenyö, David
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- 2023
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29. Proteogenomic insights suggest druggable pathways in endometrial carcinoma
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Antczak, Andrzej, Anurag, Meenakshi, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Borucki, Melissa, Cai, Shuang, Calinawan, Anna, Carr, Steven A., Castro, Patricia, Cerda, Sandra, Chan, Daniel W., Chesla, David, Cieslik, Marcin P., Cottingham, Sandra, Dhir, Rajiv, Domagalski, Marcin J., Druker, Brian J., Duffy, Elizabeth, Edwards, Nathan J., Edwards, Robert, Ellis, Matthew J., Eschbacher, Jennifer, Fam, Mina, Fevrier-Sullivan, Brenda, Francis, Jesse, Freymann, John, Gabriel, Stacey, Getz, Gad, Gillette, Michael A., Godwin, Andrew K., Goldthwaite, Charles A., Grady, Pamela, Hafron, Jason, Hariharan, Pushpa, Hindenach, Barbara, Hoadley, Katherine A., Huang, Jasmine, Ittmann, Michael M., Johnson, Ashlie, Jones, Corbin D., Ketchum, Karen A., Kirby, Justin, Le, Toan, Ma'ayan, Avi, Madan, Rashna, Mareedu, Sailaja, McGarvey, Peter B., Modugno, Francesmary, Montgomery, Rebecca, Nyce, Kristen, Paulovich, Amanda G., Pruetz, Barbara L., Qi, Liqun, Richey, Shannon, Schadt, Eric E., Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Tansil, Darlene, Thangudu, Ratna R., Tobin, Matt, Um, Ki Sung, Vatanian, Negin, Webster, Alex, Wilson, George D., Wright, Jason, Zaalishvili, Kakhaber, Zhang, Zhen, Zhao, Grace, Dou, Yongchao, Katsnelson, Lizabeth, Gritsenko, Marina A., Hu, Yingwei, Reva, Boris, Hong, Runyu, Wang, Yi-Ting, Kolodziejczak, Iga, Lu, Rita Jui-Hsien, Tsai, Chia-Feng, Bu, Wen, Liu, Wenke, Guo, Xiaofang, An, Eunkyung, Arend, Rebecca C., Bavarva, Jasmin, Chen, Lijun, Chu, Rosalie K., Czekański, Andrzej, Davoli, Teresa, Demicco, Elizabeth G., DeLair, Deborah, Devereaux, Kelly, Dhanasekaran, Saravana M., Dottino, Peter, Dover, Bailee, Fillmore, Thomas L., Foxall, McKenzie, Hermann, Catherine E., Hiltke, Tara, Hostetter, Galen, Jędryka, Marcin, Jewell, Scott D., Johnson, Isabelle, Kahn, Andrea G., Ku, Amy T., Kumar-Sinha, Chandan, Kurzawa, Paweł, Lazar, Alexander J., Lazcano, Rossana, Lei, Jonathan T., Li, Yi, Liao, Yuxing, Lih, Tung-Shing M., Lin, Tai-Tu, Martignetti, John A., Masand, Ramya P., Matkowski, Rafał, McKerrow, Wilson, Mesri, Mehdi, Monroe, Matthew E., Moon, Jamie, Moore, Ronald J., Nestor, Michael D., Newton, Chelsea, Omelchenko, Tatiana, Omenn, Gilbert S., Payne, Samuel H., Petyuk, Vladislav A., Robles, Ana I., Rodriguez, Henry, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schepmoes, Athena A., Shi, Tujin, Shi, Zhiao, Tan, Jimin, Taylor, Mason, Thiagarajan, Mathangi, Wang, Joshua M., Weitz, Karl K., Wen, Bo, Williams, C.M., Wu, Yige, Wyczalkowski, Matthew A., Yi, Xinpei, Zhang, Xu, Zhao, Rui, Mutch, David, Chinnaiyan, Arul M., Smith, Richard D., Nesvizhskii, Alexey I., Wang, Pei, Wiznerowicz, Maciej, Ding, Li, Mani, D.R., Zhang, Hui, Anderson, Matthew L., Rodland, Karin D., Zhang, Bing, Liu, Tao, and Fenyö, David
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- 2023
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30. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin
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Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Ozgun, Bavarva, Jasmin, Birger, Chet, Birrer, Michael, Calinawan, Anna, Cantley, Lewis C., Cao, Song, Carr, Steve, Ceccarelli, Michele, Chan, Daniel, Chinnaiyan, Arul, Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Mohan, Domagalski, Marcin, Dou, Yongchao, Druker, Brian, Edwards, Nathan, Ellis, Matthew, Selvan, Myvizhi Esai, Francis, Alicia, Getz, Gad, Gillette, Michael A., Robles, Tania Gonzalez, Gosline, Sara, Gümüş, Zeynep, Heiman, David, Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Iavarone, Antonio, Jaehnig, Eric, Jewel, Scott, Ji, Jiayi, Jiang, Wen, Lee Johnson, Jared, Katsnelson, Lizabeth, Ketchum, Karen, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan, Liao, Yuxing, Lindgren, Caleb, Liu, Tao, Liu, Wenke, Ma, Weiping, Rodrigues, Fernanda Martins, McKerrow, Wilson, Mesri, Mehdi, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert, Paulovich, Amanda, Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Ruggles, Kelly, Rykunov, Dmitry, Satpathy, Shankha, Savage, Sara, Schadt, Eric, Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Dick, Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik, Tan, Jimin, Terekhanova, Nadezhda, Thangudu, Ratna, Thiagarajan, Mathangi, Tignor, Nicole, Wang, Joshua, Wang, Liang-Bo, Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wu, Yige, Yao, Lijun, Yaron, Tomer M., Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Chan, Daniel W., Dhanasekaran, Saravana M., Schürer, Stephan, Smith, Richard D., Wyczalkowski, Matthew A., Liang, Wen-Wei, Lu, Rita Jui-Hsien, Jayasinghe, Reyka G., Foltz, Steven M., Porta-Pardo, Eduard, Geffen, Yifat, Wendl, Michael C., Lazcano, Rossana, Kolodziejczak, Iga, Song, Yizhe, Govindan, Akshay, Demicco, Elizabeth G., Li, Xiang, Li, Yize, Sethuraman, Sunantha, Payne, Samuel H., Fenyö, David, Rodriguez, Henry, Wiznerowicz, Maciej, Shen, Hui, Mani, D.R., Rodland, Karin D., Lazar, Alexander J., Robles, Ana I., and Ding, Li
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- 2023
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31. Multiplatform Analysis of Intratumoral PTEN Heterogeneity in Melanoma
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Chagani, Sharmeen, De Macedo, Mariana P., Carapeto, Fernando, Wang, Feng, Marzese, Diego M., Wani, Khalida, Haydu, Lauren E., Peng, Weiyi, Ong, Giang T., Warren, Sarah E., Beechem, Joseph M., Hoon, Dave S.B., Mills, Gordon B., Tetzlaff, Michael T., Lazar, Alexander J., Kwong, Lawrence N., and Davies, Michael A.
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- 2023
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32. Sentinel Lymph Node Biopsy for Extremity and Truncal Soft Tissue Sarcomas: A Systematic Review of the Literature
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Keung, Emily Z., Krause, Kate J., Maxwell, Jessica, Morris, Carol D., Crago, Aimee M., Houdek, Matthew T., Kane, John, Lewis, Valerae, Callegaro, Dario, Miller, Benjamin, Lazar, Alexander J., Gladdy, Rebecca, Raut, Chandrajit P., Fabbri, Nicola, Al-Refaie, Waddah, Fairweather, Mark, Wong, Sandra L., and Roland, Christina L.
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- 2023
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33. Re-excision After Unplanned Excision of Soft Tissue Sarcoma is Associated with High Morbidity and Limited Pathologic Identification of Residual Disease
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Traweek, Raymond S., Martin, Allison N., Rajkot, Nikita F., Guadagnolo, B. Ashleigh, Bishop, Andrew J., Lazar, Alexander J., Keung, Emily Z., Torres, Keila E., Hunt, Kelly K., Feig, Barry W., Roland, Christina L., and Scally, Christopher P.
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- 2023
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34. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
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An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Babur, Özgün, Cao, Song, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Colaprico, Antonio, Carr, Steven A., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Fenyo, David, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Iavarone, Antonio, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Kumar-Sinha, Chandan, Krug, Karsten, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, Ma, Weiping, McKerrow, Wilson, Mesri, Mehdi, Mani, D.R., Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Rodrigues, Fernanda Martins, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik P., Schürer, Stephan, Selvan, Myvizhi Esai, Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Tignor, Nicole, Thiagarajan, Mathangi, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Zhou, Daniel Cui, Geffen, Yifat, Anand, Shankara, Akiyama, Yo, Yaron, Tomer M., Song, Yizhe, Johnson, Jared L., Govindan, Akshay, Li, Yize, Huntsman, Emily, Wang, Liang-Bo, Birger, Chet, Heiman, David I., Zhang, Qing, Miller, Mendy, Maruvka, Yosef E., Haradhvala, Nicholas J., Calinawan, Anna, Belkin, Saveliy, Kerelsky, Alexander, Clauser, Karl R., Satpathy, Shankha, Payne, Samuel H., Gillette, Michael A., Dhanasekaran, Saravana M., Rodriguez, Henry, Robles, Ana I., Lazar, Alexander J., Aguet, François, Cantley, Lewis C., Ding, Li, and Getz, Gad
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- 2023
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35. Pan-cancer proteogenomics connects oncogenic drivers to functional states
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An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Calinawan, Anna, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Lei, Jonathan T., Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, McKerrow, Wilson, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Tan, Jimin, Thangudu, Ratna R., Tignor, Nicole, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Li, Yize, Porta-Pardo, Eduard, Tokheim, Collin, Bailey, Matthew H., Yaron, Tomer M., Stathias, Vasileios, Geffen, Yifat, Imbach, Kathleen J., Cao, Song, Anand, Shankara, Akiyama, Yo, Liu, Wenke, Wyczalkowski, Matthew A., Song, Yizhe, Storrs, Erik P., Wendl, Michael C., Zhang, Wubing, Sibai, Mustafa, Ruiz-Serra, Victoria, Liang, Wen-Wei, Terekhanova, Nadezhda V., Rodrigues, Fernanda Martins, Clauser, Karl R., Heiman, David I., Zhang, Qing, Aguet, Francois, Calinawan, Anna P., Dhanasekaran, Saravana M., Birger, Chet, Satpathy, Shankha, Zhou, Daniel Cui, Wang, Liang-Bo, Baral, Jessika, Johnson, Jared L., Huntsman, Emily M., Pugliese, Pietro, Colaprico, Antonio, Iavarone, Antonio, Chheda, Milan G., Ricketts, Christopher J., Fenyö, David, Payne, Samuel H., Rodriguez, Henry, Robles, Ana I., Gillette, Michael A., Kumar-Sinha, Chandan, Lazar, Alexander J., Cantley, Lewis C., Getz, Gad, and Ding, Li
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- 2023
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36. Proteogenomic data and resources for pan-cancer analysis
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Lazar, Alexander J., Paulovich, Amanda G., Colaprico, Antonio, Iavarone, Antonio, Chinnaiyan, Arul M., Druker, Brian J., Kumar-Sinha, Chandan, Newton, Chelsea J., Huang, Chen, Mani, D.R., Smith, Richard D., Huntsman, Emily, Schadt, Eric E., An, Eunkyung, Petralia, Francesca, Hostetter, Galen, Omenn, Gilbert S., Cho, Hanbyul, Rodriguez, Henry, Zhang, Hui, Kolodziejczak, Iga, Johnson, Jared L., Bavarva, Jasmin, Tan, Jimin, Rodland, Karin D., Clauser, Karl R., Krug, Karsten, Cantley, Lewis C., Wiznerowicz, Maciej, Ellis, Matthew J., Anurag, Meenakshi, Mesri, Mehdi, Gillette, Michael A., Birrer, Michael J., Ceccarelli, Michele, Dhanasekaran, Saravana M., Edwards, Nathan, Tignor, Nicole, Babur, Özgün, Pugliese, Pietro, Gosline, Sara J.C., Jewell, Scott D., Satpathy, Shankha, Chowdhury, Shrabanti, Schürer, Stephan, Carr, Steven A., Liu, Tao, Hiltke, Tara, Yaron, Tomer M., Stathias, Vasileios, Liu, Wenke, Zhang, Xu, Song, Yizhe, Zhang, Zhen, Li, Yize, Dou, Yongchao, Da Veiga Leprevost, Felipe, Geffen, Yifat, Calinawan, Anna P., Aguet, François, Akiyama, Yo, Anand, Shankara, Birger, Chet, Cao, Song, Chaudhary, Rekha, Chilappagari, Padmini, Cieslik, Marcin, Zhou, Daniel Cui, Day, Corbin, Domagalski, Marcin J., Esai Selvan, Myvizhi, Fenyö, David, Foltz, Steven M., Francis, Alicia, Gonzalez-Robles, Tania, Gümüş, Zeynep H., Heiman, David, Holck, Michael, Hong, Runyu, Hu, Yingwei, Jaehnig, Eric J., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Klein, Robert J., Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Ma, Weiping, Ma, Lei, MacCoss, Michael J., Martins Rodrigues, Fernanda, McKerrow, Wilson, Nguyen, Ngoc, Oldroyd, Robert, Pilozzi, Alexander, Reva, Boris, Rudnick, Paul, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Singhal, Deepak, Song, Xiaoyu, Storrs, Erik, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wang, Joshua M., Wang, Ying, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Xin, Yi, Yao, Lijun, Yi, Xinpei, Zhang, Qing, Zuhl, Maya, Getz, Gad, Ding, Li, Nesvizhskii, Alexey I., Wang, Pei, Robles, Ana I., Zhang, Bing, and Payne, Samuel H.
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- 2023
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37. IGF-1R/mTOR Targeted Therapy for Ewing Sarcoma: A Meta-Analysis of Five IGF-1R-Related Trials Matched to Proteomic and Radiologic Predictive Biomarkers.
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Amin, Hesham M, Morani, Ajaykumar C, Daw, Najat C, Lamhamedi-Cherradi, Salah-Eddine, Subbiah, Vivek, Menegaz, Brian A, Vishwamitra, Deeksha, Eskandari, Ghazaleh, George, Bhawana, Benjamin, Robert S, Patel, Shreyaskumar, Song, Juhee, Lazar, Alexander J, Wang, Wei-Lien, Kurzrock, Razelle, Pappo, Alberto, Anderson, Peter M, Schwartz, Gary K, Araujo, Dejka, Cuglievan, Branko, Ratan, Ravin, McCall, David, Mohiuddin, Sana, Livingston, John A, Molina, Eric R, Naing, Aung, and Ludwig, Joseph A
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Ewing sarcoma ,PET/CT ,biological therapies ,biomarker ,drug response ,pIGF-1R ,PET ,CT ,Oncology and Carcinogenesis - Abstract
Background : Ten to fourteen percent of Ewing sarcoma (ES) study participants treated nationwide with IGF-1 receptor (IGF-1R)-targeted antibodies achieved tumor regression. Despite this success, low response rates and short response durations (approximately 7-weeks) have slowed the development of this therapy. Methods: We performed a meta-analysis of five phase-1b/2 ES-oriented trials that evaluated the anticancer activity of IGF-1R antibodies +/- mTOR inhibitors (mTORi). Our meta-analysis provided a head-to-head comparison of the clinical benefits of IGF-1R antibodies vs. the IGF-1R/mTOR-targeted combination. Available pretreatment clinical samples were semi-quantitatively scored using immunohistochemistry to detect proteins in the IGF-1R/PI3K/AKT/mTOR pathway linked to clinical response. Early PET/CT imaging, obtained within the first 2 weeks (median 10 days), were examined to determine if reduced FDG avidity was predictive of progression-free survival (PFS). Results: Among 56 ES patients treated at MD Anderson Cancer Center (MDACC) with IGF-1R antibodies, our analysis revealed a significant ~two-fold improvement in PFS that favored a combination of IGF-1R/mTORi therapy (1.6 vs. 3.3-months, p = 0.042). Low pIGF-1R in the pretreatment specimens was associated with treatment response. Reduced total-lesion glycolysis more accurately predicted the IGF-1R response than other previously reported radiological biomarkers. Conclusion: Synergistic drug combinations, and newly identified proteomic or radiological biomarkers of IGF-1R response, may be incorporated into future IGF-1R-related trials to improve the response rate in ES patients.
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- 2020
38. Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer
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Carrot-Zhang, Jian, Chambwe, Nyasha, Damrauer, Jeffrey S, Knijnenburg, Theo A, Robertson, A Gordon, Yau, Christina, Zhou, Wanding, Berger, Ashton C, Huang, Kuan-lin, Newberg, Justin Y, Mashl, R Jay, Romanel, Alessandro, Sayaman, Rosalyn W, Demichelis, Francesca, Felau, Ina, Frampton, Garrett M, Han, Seunghun, Hoadley, Katherine A, Kemal, Anab, Laird, Peter W, Lazar, Alexander J, Le, Xiuning, Oak, Ninad, Shen, Hui, Wong, Christopher K, Zenklusen, Jean C, Ziv, Elad, Network, Cancer Genome Atlas Analysis, Aguet, Francois, Ding, Li, Demchok, John A, Mensah, Michael KA, Caesar-Johnson, Samantha, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Alfoldi, Jessica, Karczewski, Konrad J, MacArthur, Daniel G, Meyerson, Matthew, Benz, Christopher, Stuart, Joshua M, Cherniack, Andrew D, and Beroukhim, Rameen
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Biological Sciences ,Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Genetics ,Human Genome ,Clinical Research ,Cancer ,Biotechnology ,DNA Methylation ,DNA-Binding Proteins ,Ethnicity ,F-Box-WD Repeat-Containing Protein 7 ,Gene Expression Regulation ,Neoplastic ,Genetic Predisposition to Disease ,Genetics ,Population ,Genome ,Human ,Genomics ,High-Throughput Nucleotide Sequencing ,Humans ,MicroRNAs ,Mutation ,Neoplasm Proteins ,Neoplasms ,Transcription Factors ,Von Hippel-Lindau Tumor Suppressor Protein ,Cancer Genome Atlas Analysis Network ,TCGA ,admixture ,ancestry ,cancer ,eQTL ,genomics ,mRNA ,methylation ,miRNA ,mutation ,Neurosciences ,Oncology & Carcinogenesis ,Biochemistry and cell biology ,Oncology and carcinogenesis - Abstract
We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer Genome Atlas. We demonstrated that cancer subtypes and ancestry-related technical artifacts are important confounders that have been insufficiently accounted for. Once accounted for, ancestry-associated differences spanned all molecular features and hundreds of genes. Biologically significant differences were usually tissue specific but not specific to cancer. However, admixture and pathway analyses suggested some of these differences are causally related to cancer. Specific findings included increased FBXW7 mutations in patients of African origin, decreased VHL and PBRM1 mutations in renal cancer patients of African origin, and decreased immune activity in bladder cancer patients of East Asian origin.
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- 2020
39. Pan-cancer analysis of whole genomes
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Campbell, Peter J, Getz, Gad, Korbel, Jan O, Stuart, Joshua M, Jennings, Jennifer L, Stein, Lincoln D, Perry, Marc D, Nahal-Bose, Hardeep K, Ouellette, BF Francis, Li, Constance H, Rheinbay, Esther, Nielsen, G Petur, Sgroi, Dennis C, Wu, Chin-Lee, Faquin, William C, Deshpande, Vikram, Boutros, Paul C, Lazar, Alexander J, Hoadley, Katherine A, Louis, David N, Dursi, L Jonathan, Yung, Christina K, Bailey, Matthew H, Saksena, Gordon, Raine, Keiran M, Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun, Wang, Wenyi, Wheeler, David A, Ding, Li, Simpson, Jared T, O'Connor, Brian D, Yakneen, Sergei, Ellrott, Kyle, Miyoshi, Naoki, Butler, Adam P, Royo, Romina, Shorser, Solomon I, Vazquez, Miguel, Rausch, Tobias, Tiao, Grace, Waszak, Sebastian M, Rodriguez-Martin, Bernardo, Shringarpure, Suyash, Wu, Dai-Ying, Demidov, German M, Delaneau, Olivier, Hayashi, Shuto, Imoto, Seiya, Habermann, Nina, Segre, Ayellet V, Garrison, Erik, Cafferkey, Andy, Alvarez, Eva G, Maria Heredia-Genestar, Jose, Muyas, Francesc, Drechsel, Oliver, Bruzos, Alicia L, Temes, Javier, Zamora, Jorge, Baez-Ortega, Adrian, Kim, Hyung-Lae, Mashl, R Jay, Ye, Kai, DiBiase, Anthony, Huang, Kuan-lin, Letunic, Ivica, McLellan, Michael D, Newhouse, Steven J, Shmaya, Tal, Kumar, Sushant, Wedge, David C, Wright, Mark H, Yellapantula, Venkata D, Gerstein, Mark, Khurana, Ekta, Marques-Bonet, Tomas, Navarro, Arcadi, Bustamante, Carlos D, Siebert, Reiner, Nakagawa, Hidewaki, Easton, Douglas F, Ossowski, Stephan, Tubio, Jose MC, De La Vega, Francisco M, Estivill, Xavier, Yuen, Denis, Mihaiescu, George L, Omberg, Larsson, Ferretti, Vincent, Sabarinathan, Radhakrishnan, Pich, Oriol, Gonzalez-Perez, Abel, Weiner, Amaro Taylor, Fittall, Matthew W, Demeulemeester, Jonas, Tarabichi, Maxime, and Roberts, Nicola D
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Biological Sciences ,Biomedical and Clinical Sciences ,Bioinformatics and Computational Biology ,Genetics ,Oncology and Carcinogenesis ,Cancer Genomics ,Biotechnology ,Human Genome ,Cancer ,Prevention ,2.1 Biological and endogenous factors ,Cell Proliferation ,Cellular Senescence ,Chromothripsis ,Cloud Computing ,DNA Mutational Analysis ,Evolution ,Molecular ,Female ,Genome ,Human ,Genomics ,Germ-Line Mutation ,High-Throughput Nucleotide Sequencing ,Humans ,Information Dissemination ,Male ,Mutagenesis ,Mutation ,Neoplasms ,Oncogenes ,Promoter Regions ,Genetic ,RNA Splicing ,Reproducibility of Results ,Telomerase ,Telomere ,ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium ,General Science & Technology - Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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- 2020
40. B cells and tertiary lymphoid structures promote immunotherapy response
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Helmink, Beth A, Reddy, Sangeetha M, Gao, Jianjun, Zhang, Shaojun, Basar, Rafet, Thakur, Rohit, Yizhak, Keren, Sade-Feldman, Moshe, Blando, Jorge, Han, Guangchun, Gopalakrishnan, Vancheswaran, Xi, Yuanxin, Zhao, Hao, Amaria, Rodabe N, Tawbi, Hussein A, Cogdill, Alex P, Liu, Wenbin, LeBleu, Valerie S, Kugeratski, Fernanda G, Patel, Sapna, Davies, Michael A, Hwu, Patrick, Lee, Jeffrey E, Gershenwald, Jeffrey E, Lucci, Anthony, Arora, Reetakshi, Woodman, Scott, Keung, Emily Z, Gaudreau, Pierre-Olivier, Reuben, Alexandre, Spencer, Christine N, Burton, Elizabeth M, Haydu, Lauren E, Lazar, Alexander J, Zapassodi, Roberta, Hudgens, Courtney W, Ledesma, Deborah A, Ong, SuFey, Bailey, Michael, Warren, Sarah, Rao, Disha, Krijgsman, Oscar, Rozeman, Elisa A, Peeper, Daniel, Blank, Christian U, Schumacher, Ton N, Butterfield, Lisa H, Zelazowska, Monika A, McBride, Kevin M, Kalluri, Raghu, Allison, James, Petitprez, Florent, Fridman, Wolf Herman, Sautès-Fridman, Catherine, Hacohen, Nir, Rezvani, Katayoun, Sharma, Padmanee, Tetzlaff, Michael T, Wang, Linghua, and Wargo, Jennifer A
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Immunization ,Cancer ,Vaccine Related ,Genetics ,B-Lymphocytes ,Biomarkers ,Tumor ,Carcinoma ,Renal Cell ,Cell Cycle Checkpoints ,Clone Cells ,Dendritic Cells ,Follicular ,Gene Expression Regulation ,Neoplastic ,Humans ,Immunologic Memory ,Immunotherapy ,Mass Spectrometry ,Melanoma ,Neoplasm Metastasis ,Phenotype ,Prognosis ,RNA-Seq ,Receptors ,Immunologic ,Single-Cell Analysis ,T-Lymphocytes ,Tertiary Lymphoid Structures ,Transcriptome ,General Science & Technology - Abstract
Treatment with immune checkpoint blockade (ICB) has revolutionized cancer therapy. Until now, predictive biomarkers1-10 and strategies to augment clinical response have largely focused on the T cell compartment. However, other immune subsets may also contribute to anti-tumour immunity11-15, although these have been less well-studied in ICB treatment16. A previously conducted neoadjuvant ICB trial in patients with melanoma showed via targeted expression profiling17 that B cell signatures were enriched in the tumours of patients who respond to treatment versus non-responding patients. To build on this, here we performed bulk RNA sequencing and found that B cell markers were the most differentially expressed genes in the tumours of responders versus non-responders. Our findings were corroborated using a computational method (MCP-counter18) to estimate the immune and stromal composition in this and two other ICB-treated cohorts (patients with melanoma and renal cell carcinoma). Histological evaluation highlighted the localization of B cells within tertiary lymphoid structures. We assessed the potential functional contributions of B cells via bulk and single-cell RNA sequencing, which demonstrate clonal expansion and unique functional states of B cells in responders. Mass cytometry showed that switched memory B cells were enriched in the tumours of responders. Together, these data provide insights into the potential role of B cells and tertiary lymphoid structures in the response to ICB treatment, with implications for the development of biomarkers and therapeutic targets.
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- 2020
41. Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome
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Simpson, Rebecca C., Shanahan, Erin R., Batten, Marcel, Reijers, Irene L. M., Read, Mark, Silva, Ines P., Versluis, Judith M., Ribeiro, Rosilene, Angelatos, Alexandra S., Tan, Jian, Adhikari, Chandra, Menzies, Alexander M., Saw, Robyn P. M., Gonzalez, Maria, Shannon, Kerwin F., Spillane, Andrew J., Velickovic, Rebecca, Lazar, Alexander J., Damania, Ashish V., Mishra, Aditya K., Chelvanambi, Manoj, Banerjee, Anik, Ajami, Nadim J., Wargo, Jennifer A., Macia, Laurence, Holmes, Andrew J., Wilmott, James S., Blank, Christian U., Scolyer, Richard A., and Long, Georgina V.
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- 2022
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42. Androgen receptor blockade promotes response to BRAF/MEK-targeted therapy
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Vellano, Christopher P., White, Michael G., Andrews, Miles C., Chelvanambi, Manoj, Witt, Russell G., Daniele, Joseph R., Titus, Mark, McQuade, Jennifer L., Conforti, Fabio, Burton, Elizabeth M., Lastrapes, Matthew J., Ologun, Gabriel, Cogdill, Alexandria P., Morad, Golnaz, Prieto, Peter, Lazar, Alexander J., Chu, Yanshuo, Han, Guangchun, Khan, M. A. Wadud, Helmink, Beth, Davies, Michael A., Amaria, Rodabe N., Kovacs, Jeffrey J., Woodman, Scott E., Patel, Sapna, Hwu, Patrick, Peoples, Michael, Lee, Jeffrey E., Cooper, Zachary A., Zhu, Haifeng, Gao, Guang, Banerjee, Hiya, Lau, Mike, Gershenwald, Jeffrey E., Lucci, Anthony, Keung, Emily Z., Ross, Merrick I., Pala, Laura, Pagan, Eleonora, Segura, Rossana Lazcano, Liu, Qian, Borthwick, Mikayla S., Lau, Eric, Yates, Melinda S., Westin, Shannon N., Wani, Khalida, Tetzlaff, Michael T., Haydu, Lauren E., Mahendra, Mikhila, Ma, XiaoYan, Logothetis, Christopher, Kulstad, Zachary, Johnson, Sarah, Hudgens, Courtney W., Feng, Ningping, Federico, Lorenzo, Long, Georgina V., Futreal, P. Andrew, Arur, Swathi, Tawbi, Hussein A., Moran, Amy E., Wang, Linghua, Heffernan, Timothy P., Marszalek, Joseph R., and Wargo, Jennifer A.
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- 2022
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43. Experimental models of undifferentiated pleomorphic sarcoma and malignant peripheral nerve sheath tumor
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Bhalla, Angela D., Landers, Sharon M., Singh, Anand K., Landry, Jace P., Yeagley, Michelle G., Myerson, Gabryella S. B., Delgado-Baez, Cristian B., Dunnand, Stephanie, Nguyen, Theresa, Ma, Xiaoyan, Bolshakov, Svetlana, Menegaz, Brian A., Lamhamedi-Cherradi, Salah-Eddine, Mao, Xizeng, Song, Xingzhi, Lazar, Alexander J., McCutcheon, Ian E., Slopis, John M., Ludwig, Joseph A., Lev, Dina C., Rai, Kunal, and Torres, Keila E.
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- 2022
- Full Text
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44. Final Safety and Health-Related Quality of LIfe Results of the Phase 2/3 Act.In.Sarc Study With Preoperative NBTXR3 Plus Radiation Therapy Versus Radiation Therapy in Locally Advanced Soft-Tissue Sarcoma
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Bonvalot, Sylvie, Rutkowski, Piotr L., Thariat, Juliette, Carrère, Sébastien, Ducassou, Anne, Sunyach, Marie-Pierre, Agoston, Peter, Hong, Angela M., Mervoyer, Augustin, Rastrelli, Marco, Moreno, Victor, Li, Rubi K., Tiangco, Béatrice J., Casado Herráez, Antonio, Gronchi, Alessandro, Sy-Ortin, Teresa, Hohenberger, Peter, de Baère, Thierry, Cesne, Axel Le, Helfre, Sylvie, Saada-Bouzid, Esma, Anghel, Rodica M., Kantor, Guy, Montero, Angel, Loong, Herbert H., Vergés, Ramona, Kacso, Gabriel, Austen, Lyn, Servois, Vincent F., Wardelmann, Eva, Dimitriu, Mikaela, Said, Patricia, Lazar, Alexander J., Bovée, Judith V.M.G., Le Péchoux, Cécile, and Pápai, Zsusanna
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- 2022
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45. Durvalumab plus tremelimumab in advanced or metastatic soft tissue and bone sarcomas: a single-centre phase 2 trial
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Somaiah, Neeta, Conley, Anthony P, Parra, Edwin Roger, Lin, Heather, Amini, Behrang, Solis Soto, Luisa, Salazar, Ruth, Barreto, Carmelia, Chen, Honglei, Gite, Swati, Haymaker, Cara, Nassif, Elise F, Bernatchez, Chantale, Mitra, Akash, Livingston, John Andrew, Ravi, Vinod, Araujo, Dejka M, Benjamin, Robert, Patel, Shreyaskumar, Zarzour, Maria A, Sabir, Sharjeel, Lazar, Alexander J, Wang, Wei-Lien, Daw, Najat C, Zhou, Xiao, Roland, Christina L, Cooper, Zachary A, Rodriguez-Canales, Jaime, Futreal, Andrew, Soria, Jean-Charles, Wistuba, Ignacio I, and Hwu, Patrick
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- 2022
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46. Update from the 5th Edition of the World Health Organization Classification of Head and Neck Tumors: Familial Tumor Syndromes
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Nosé, Vania and Lazar, Alexander J.
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- 2022
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47. Challenges associated with the integration of immuno-oncology agents in clinical practice
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Lazure, Patrice, Parikh, Aparna R., Ready, Neal E., Davies, Marianne J., Péloquin, Sophie, Caterino, Jeffrey M., Lewandowski, Robert, Lazar, Alexander J., and Murray, Suzanne
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- 2022
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48. Multi-modal molecular programs regulate melanoma cell state
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Andrews, Miles C., Oba, Junna, Wu, Chang-Jiun, Zhu, Haifeng, Karpinets, Tatiana, Creasy, Caitlin A., Forget, Marie-Andrée, Yu, Xiaoxing, Song, Xingzhi, Mao, Xizeng, Robertson, A. Gordon, Romano, Gabriele, Li, Peng, Burton, Elizabeth M., Lu, Yiling, Sloane, Robert Szczepaniak, Wani, Khalida M., Rai, Kunal, Lazar, Alexander J., Haydu, Lauren E., Bustos, Matias A., Shen, Jianjun, Chen, Yueping, Morgan, Margaret B., Wargo, Jennifer A., Kwong, Lawrence N., Haymaker, Cara L., Grimm, Elizabeth A., Hwu, Patrick, Hoon, Dave S. B., Zhang, Jianhua, Gershenwald, Jeffrey E., Davies, Michael A., Futreal, P. Andrew, Bernatchez, Chantale, and Woodman, Scott E.
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- 2022
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49. Multi-site desmoplastic small round cell tumors are genetically related and immune-cold
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Wu, Chia-Chin, Beird, Hannah C., Lamhamedi-Cherradi, Salah-Eddine, Soeung, Melinda, Ingram, Davis, Truong, Danh D., Porter, Robert W., Krishnan, Sandhya, Little, Latasha, Gumbs, Curtis, Zhang, Jianhua, Titus, Mark, Genovese, Giannicola, Ludwig, Joseph A., Lazar, Alexander J., Hayes-Jordan, Andrea, and Futreal, P. Andrew
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- 2022
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50. The androgen receptor is a therapeutic target in desmoplastic small round cell sarcoma
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Lamhamedi-Cherradi, Salah-Eddine, Maitituoheti, Mayinuer, Menegaz, Brian A., Krishnan, Sandhya, Vetter, Amelia M., Camacho, Pamela, Wu, Chia-Chin, Beird, Hannah C., Porter, Robert W., Ingram, Davis R., Ramamoorthy, Vandhana, Mohiuddin, Sana, McCall, David, Truong, Danh D., Cuglievan, Branko, Futreal, P. Andrew, Velasco, Alejandra Ruiz, Anvar, Nazanin Esmaeili, Utama, Budi, Titus, Mark, Lazar, Alexander J., Wang, Wei-Lien, Rodriguez-Aguayo, Cristian, Ratan, Ravin, Livingston, J. Andrew, Rai, Kunal, MacLeod, A. Robert, Daw, Najat C., Hayes-Jordan, Andrea, and Ludwig, Joseph A.
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- 2022
- Full Text
- View/download PDF
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